loop order doesn't matter. water cooling works by creating a "constant" temperature exchange, meaning once the flow of water is started, temperatures remain constant so long as pump speed and fan speeds remain constant. changing the order of the hardware in the loop will only add or subtract a degree or two at most and will not change the problem he is having. the only things I can think of that would cause abnormally high temperatures (+10-15'C higher than what they should be) would be:
(This is after taking into account all of his posts in this thread)
faulty pump
flow restriction